[BioC] Q-value question

[James W. MacDonald]

Hi Guido,

Guido Leoni wrote:
> Dear List
> I'm new to microarrays analysis. I'm analyzing an experiment with 2
> condtions and 3 microarrays for condition. My data are succesfully
> normalized and I have a list of gene modulated with aFC, a raw p-value and a
> q-value. My q-value are never lower than 0,1. If I well understand my
> q-value is the minimum false discovery rate for which my FC are
> statistically significant. So have I set a threshold similar to p-value to
> select my differentially regulated genes? if yes (what does mean the fact
> that my q-value is never lower than 0,1?)
> Sorry for my confused question and
> Thank you for every tips you could give to me

The FDR is an estimate of the maximum percentage of 'significant' 
results that are false positives. So for instance, if you accept all the 
genes (reporters) with a q-value =< 0.1, then the assumption is that 
somewhere around 10% of those are false positives.

So when you go to validate those genes (if you use that FDR level), you 
can expect about 10% or so to fail to validate. This of course assumes 
that all the assumptions have been met blah blah statistics statistics 
statistics... ;-D

Best,

Jim


> 

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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